Objective: To analyze the effects of basic periodontal treatment on the subgingival microflora of patients over 65 years old with diabetes mellitus and chronic periodontitis (DMCP) by high throughput sequencing technology and to analyze the mechanism of oxidative stress. Methods: A total of 100 DMCP patients over 65 years old were selected as the research subjects and randomly divided into a study group and a control group, with 50 cases in each group. The patients in the control group were treated with the routine treatments, such as intensive blood glucose control, symptomatic treatment of basic diseases and oral health knowledge education while the patients in the study group were treated with periodontal basic treatment on this basis. The treatments and follow-up visit were completed within 4 weeks. The baseline data between the 2 groups were compared; the relative contents of periodontal subgingival bacteria before and at 3 months after the treatments between the 2 groups were compared by high-throughput sequencing technology. Results: Two patients in the study group and 5 patients in the control group were lost to follow-up, and finally 48 patients and 45 patients were included. There was no significant difference in baseline data between the 2 groups (P>0.05). There was no significant difference between the 2 groups in the relative contents of various pathogenic bacteria in the periodontal subgingival microflora and the levels of various oxidizing and reducing agents in the gingival crevicular fluid before treatment (P>0.05). Three months after the treatment, the relative contents of all kinds of pathogenic bacteria in periodontal subgingival flora of 2 groups were decreased compared with that before treatment, and the differences were statistically significant (P>0.05). The relative contents of all kinds of pathogenic bacteria in periodontal subgingival flora of the study group were lower than that of the control group, and the differences were statistically significant (P>0.05). Conclusion: The application of periodontal basic treatment can significantly reduce the contents of pathogenic bacteria in periodontal subgingival microflora of the patients with DMCP, and correct the imbalance of oral microflora.